sliding.window.transform-methods: Sliding Window Transformation

In pievos101/PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Sliding Window Transformation

Description

This generic function transforms an existing object of class "GENOME" into another object of class "GENOME", in which each region corresponds to one window. This allows to apply the full spectrum of PopGenome methods to sliding window data.

Usage

## S4 method for signature 'GENOME'
sliding.window.transform(object, 
	width=7, jump=5, 
	type=1,
	start.pos=FALSE,end.pos=FALSE,
	whole.data=TRUE
	)

Arguments

object	an object of class "GENOME"
width	window size. default:7
jump	jump size. default:5
type	1 scan only biallelic positions (SNPs), 2 scan the genome. default:1
start.pos	start position
end.pos	end position
whole.data	scan the complete data by concatenating the regions in "object". If FALSE, each region is scanned seperately.

Value

The function creates a transformed object of class "GENOME".

Note

If you want to scan regions seperately (whole.data=FALSE), you may not use the big.data option in the readData function. PopGenome will scan the data from position 1 to the last observed SNP if start or end-positions are not specified.

Examples

# GENOME.class       <- readData("...\Alignments")
# slide.GENOME.class <- sliding.window.transform(GENOME.class)
# slide.GENOME.class <- sliding.window.transform(GENOME.class,100,100)
# slide.GENOME.class <- neutrality.stats(slide.GENOME.class)
# [e-mail]
# values             <- get.neutrality(slide.GENOME.class)
# GENOME.class       <- readSNP("Arabidopsis", CHR=1)
# GENOME.slide       <- sliding.window.transform(GENOME.split, 10000, 10000, type=2,
# start.pos=10000000, end.pos=12000000)
# [e-mail]

pievos101/PopGenome documentation built on Feb. 24, 2023, 7:11 a.m.